Why are some faces in my mesh darker?
Check your normals. If some of the facess are turned inside out, pointing inward into the inside of the mesh, they can be seen as dark areas.
Before recalculate normals (in the toolbar (N) in the 3D View, or CtrlN):

After recalculate normals.

Note that normals will only be recalculated for selected faces, so you probably want to select all (A) before recalculating.